Maybe not Joseph Gordon-Levitt? And maybe Killer Croc?
Tom Hardy, who you may remember as the clone of Picard from the terrible Star Trek: Nemesis but hopefully remember as the forger from the not-at-all-terrible Inception, is reportedly taking on a major role in Batman 3. No word on who he'll be playing or if it's a villain, but everyone is jumping to the conclusion that he'll play the Riddler. I'm not sure about that.
Earlier rumors about Joseph Gordon-Levitt were based on some word that an Inception cast member would be following Christopher Nolan to the next Batman movie. So it sounds like Joseph-Gordon Levitt is out and Tom Hardy is in.
None of this is concrete, but I'd say Tom Hardy being in the movie is very likely at this point. Joseph Gordon-Levitt could be involved or not, Killer Croc could be the main villain or a minor villain or not in it at all.
After The Scarecrow, Ra's Al Ghul, The Joker, and Two-Face, who should be Batman's next enemy in the Batman Begins/The Dark Knight series? Well, as of now we know that Tom Hardy will play Bane and Anne Hathaway will play Catwoman.
Check out the master list for all the villains covered. I've pretty much run out by now. Obviously, there are more Batman villains, but not any of significance that I know of. As of February 2009, no one is confirmed as a villain. Not the Johnny Depp Riddler, not Phillip Seymour Hoffman Penguin, nobody.